rs2188962

Variant names:

• chr5-132435113-C-T
• rs2188962
• ENST00000638452.2:c.-208-14537C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000638452.2(ENSG00000283782):​c.-208-14537C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.282 in 152,136 control chromosomes in the GnomAD database, including 7,798 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.28 (7798 hom., cov: 31)
• Consequence: ENSG00000283782 ENST00000638452.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43
• Publications: 149 publications found

Genes affected

ENSG00000283782 (HGNC:):

CARINH (HGNC:33838): (colitis associated IRF1 antisense regulator of intestinal homeostasis)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.408 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CARINH	NR_161242.1	n.232-14537C>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000283782	ENST00000638452.2	c.-208-14537C>T		intron_variant	Intron 2 of 26	5		ENSP00000492349.2

Frequencies

GnomAD3 genomes AF: 0.282 AC: 42919 AN: 152018 Hom.: 7801 Cov.: 31

Gnomad AFR AF: 0.0917

Gnomad AMI AF: 0.620

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.00270

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.334

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.282 AC: 42910 AN: 152136 Hom.: 7798 Cov.: 31 AF XY: 0.272 AC XY: 20192 AN XY: 74372

African (AFR) AF: 0.0915 AC: 3802 AN: 41532

American (AMR) AF: 0.297 AC: 4543 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.410 AC: 1424 AN: 3470

East Asian (EAS) AF: 0.00270 AC: 14 AN: 5180

South Asian (SAS) AF: 0.110 AC: 530 AN: 4822

European-Finnish (FIN) AF: 0.309 AC: 3267 AN: 10572

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.412 AC: 28013 AN: 67970

Other (OTH) AF: 0.329 AC: 694 AN: 2110

Alfa AF: 0.380 Hom.: 46970

Bravo AF: 0.277

Asia WGS AF: 0.0600 AC: 208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.77
DANN	Benign	0.50
PhyloP100		-1.4

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2188962; hg19: chr5-131770805;